Questions tagged [atomic-simulation-environment]

For questions about the Atomic Simulation Environment (ASE) tools and Python modules

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How to Change the Color Palette of Atoms in ASE GUI

I know that there is a configuration file called gui.py that would be initialized if it is placed in a directory like ...
Jaafar Mehrez's user avatar
3 votes
1 answer
75 views

Controlling Initial Velocities in NVE Trajectory Simulations with VASP

"I've determined the initial velocities of the surface following its equilibration at 300 K in the NVT ensemble. Now, I aim to conduct AIMD (NVE ensemble)with the metal surface (initially defined ...
Rubi Agrawal's user avatar
3 votes
1 answer
74 views

Making Deuterium POTCAR file for optimization in VASP software

How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
Rubi Agrawal's user avatar
1 vote
0 answers
81 views

Disappearing vacuum layer when relaxing bilayered hBN with VASP

I'm doing geometry optimization of bilayer h-BN, a 72-atom supercell (6x6x1) with vacuum thickness of 20 Å, and I set the parameters in INCAR as below: ...
Meifeng WANG's user avatar
1 vote
0 answers
37 views

Interstitial and vacancy defects

I'm trying to insert interstitial defects in an FCC crystal with 32 atoms. And also a quick way of inserting a vacancy or doing a substitutional defect. Any code for this would be deeply appreciated. ...
Nana Kofi Boakye's user avatar
6 votes
1 answer
524 views

pyscf: Why should the choice of pseudopotential determine the total energy, and not the physics?

I have limited experience with DFT, but as an exercise I have written a DFT program of an atom (from scratch using nothing more than python built in functions and numpy) by following Richard Martin's ...
Mikke Mus's user avatar
  • 163
2 votes
1 answer
44 views

How to make initial trajectory for incident A2 molecule on any surface?

I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
Rubi Agrawal's user avatar
2 votes
1 answer
91 views

How to make a super cell for molecular crystal with PBC

I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
Pradip Si's user avatar
2 votes
1 answer
51 views

Visualizing magnetic moments of Quantum espresso input/output files

I am looking for a software/website that can visualize atomic structure of my quantum espresso input/output files with magnetic moments. Any help will be highly appreciated. Thanks in advance!
rahman62's user avatar
  • 143
3 votes
0 answers
86 views

How to model the final state for NEB calculations in ASE

I want to find the transition state properties (activation energy, reaction rate and few thermodynamic properties). I found out that NEB can do the transition state search. I have already created the ...
sachin hegde's user avatar
4 votes
1 answer
104 views

How to use ase gui to visualize the geometry optimization (through graphs and animation)?

How can I visualize the geometry optimization? I want to see the plot of potential energy through various iterations to reach the minimum value. I would also like to see the animation of the atoms ...
sachin hegde's user avatar
1 vote
2 answers
73 views

ModuleNotFoundError: No module named 'ase.mep'

I am trying to find the transition path using NEB method in ASE. However when i try to import the ase.mep module, i am getting the following error 'ModuleNotFoundError: No module named 'ase.mep'' Can ...
sachin hegde's user avatar
3 votes
2 answers
120 views

How to model adsorbate layer on a monolayer graphene surface using ASE

My surface is a monolayer graphene. I want to add a layer of water as adsorbate and the parameters are height = 3.31 Angstroms on top of the slab; Coverage = 24/72; The orientation is: The hydrogen ...
sachin hegde's user avatar
3 votes
0 answers
51 views

Beginning in molecular simulation world

I want to do a simulation of an atom (type atom is not important) bouncing inside a spherical surface (the material of the surface is not important too) (i.e. starting from an initial velocity, the ...
eraldcoil's user avatar
  • 201
5 votes
1 answer
161 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
5 votes
2 answers
73 views

ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object

I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer. ...
Samaray's user avatar
  • 61
1 vote
1 answer
29 views

ASE reading cell dimensions from XYZ file generated by I-Py

I have an xyz file formatted in the following way (just a snapshot of the 192 atoms is shown) its cell information is given in # ...
KugelBlitz's user avatar
4 votes
1 answer
199 views

Random velocity generation

How to generate random velocities in the geometry coordinates of a surface (POSCAR file) using the Boltzmann distribution law with Atomic Simulation Environment (ASE) or other codes for Molecular ...
Rubi Agrawal's user avatar
3 votes
1 answer
116 views

Print full stress tensor in ASE to calculate Green Kubo viscosity

I would like to print out the off diagonal components of the full stress tensor in ASE. The goal is then to calculate the Green Kubo viscosity. One should use the ensemble average of the off diagonal ...
Marco Di Gennaro's user avatar
2 votes
0 answers
71 views

Water simulation in ASE/LAMMPS

I want to simulate some water in MD with ASE and a LammpsLib calculator. I set up a minimal Lammps calculator and I try to calculate the energy per atom of an isolated molecule, and a 3x3x3 supercell. ...
Marco Di Gennaro's user avatar
3 votes
0 answers
112 views

Read and run lammps water model in ASE

I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly. ASE is not able to read the <...
Marco Di Gennaro's user avatar
2 votes
0 answers
47 views

What is the best model to calculate the free energies using ASE thermochemistry?

I am trying to calculate the free energy of adsorption of a small molecule on a 2D material. After adsorption, I am using the thermochemistry module of the Atomic Simulation Environment to calculate ...
ansonthms's user avatar
  • 921
4 votes
0 answers
86 views

ASE/XTB: zero temperature and stress in MD simulation

I want to see how the volume and pressure of my cell is changing during a MD relaxation in ASE. I used the atom.get_volume() and ...
Marco Di Gennaro's user avatar
3 votes
0 answers
58 views

Are then any material property solvers (from Charge Density) available in python?

I am looking to predict properties like the Bulk Modulus, total energy, etc., all from the charge density I have as input (CHGCAR file)
Pranoy Ray's user avatar
  • 1,611
4 votes
1 answer
203 views

ASE: Shape mismatch when using FrechetCellFilter filter

I want to use a FrechetCellFilter into a MD simulation with ASE to make sure both the atomic forces and unit cell are simultaneously minimised. I encounter a ...
Marco Di Gennaro's user avatar
4 votes
1 answer
358 views

How to put adsorbate on the surface by ASE

I would like to make formate-adsorbed surface on Cu(111). I have prepared the Cu(111) by ASE: ...
Tommy Wang's user avatar
5 votes
1 answer
141 views

How to read multiple Atoms objects from a single file using ASE

I am trying to read Atoms objects from the file "data.txt", which contains multiple configurations. Each configuration has a different cell. ...
user174967's user avatar
4 votes
1 answer
87 views

How to get displacements along VASP NEB trajectory?

I am performing an NEB calculation with VASP and VTST. I would like to visualize the atoms along the path and to calculate their displacements. When I have a single relaxation's XDATCAR, I can unwrap ...
kpoint's user avatar
  • 139
4 votes
1 answer
205 views

Run ASE MD in parallel

I would like to run my MD simulation in parallel on a cluster (16 CPUs per node). From the ASE doc we can see that: ASE will automatically run in parallel, if it can import an MPI communicator from ...
Marco Di Gennaro's user avatar
3 votes
0 answers
142 views

How to check the units from ASE get_forces() function?

Here is a little python code that loops through a molecular dynamics trajectory (performed with the ASE package) and outputs the forces on the atoms at each frame: ...
breadcrumbs's user avatar
5 votes
1 answer
155 views

Fix layers of a slab

How do you fix the bottom layers of a slab to mimic a bulk material in ASE? Any functional that takes the slab object and writes a POSCAR with selective dynamics will be deeply appreciated. Thank you.
Nana Kofi Boakye's user avatar
2 votes
0 answers
192 views

ASE write extxyz question

I'm trying to convert vasp outcar to extxyz using ase read and write. But how can I control what contents to print out from comment line and data columns? For example, I hope to convert vasp AIMD ...
exsonic01's user avatar
  • 843
10 votes
3 answers
612 views

Tool to extract rings from zeolite structures

I am trying to reproduce the work done in this paper https://doi.org/10.1021/acscatal.7b00588. In this direction, I have been successful in optimizing the unit cells of the zeolites. For further steps,...
ansonthms's user avatar
  • 921
3 votes
1 answer
125 views

Python code for combining two surfaces to form an interface

I have two surfaces named POSCAR1 and POSCAR2. I want to stack the surface of POSCAR2 on POSCAR1 to form an interface and also to match their lattice constants. I tried a solution here by adding it ...
Nana Kofi Boakye's user avatar
4 votes
2 answers
111 views

How to Create a 2D Structure of Boron (Brophene) using ASE?

Unlike Graphene and MoS2, For borophene, I didn't find any inbuilt function in ASE. I have tried to make it, but i failed. So If anyone could help me, it will be great help. Since brophene has ...
Akshit Dhillon's user avatar
2 votes
1 answer
111 views

Generate a bimetallic surface in ASE

I am trying to generate a 50-50 Pt-Au fcc(111) bimetallic surface in ASE for DFT calcualtions. However, I am unable to figure out the procedure. Any help regarding the procedure will be great. Thanks
ARKA PRAVA SARKAR's user avatar
2 votes
1 answer
324 views

How can I load the xyz file correctly by ase?

The format of xyz file is as follow. ...
peng liu's user avatar
3 votes
1 answer
361 views

How to read a poscar file which is a surface and add adsorbates using ASE

I have a POSCAR file containing Co, Cr, Fe, Ni elements. It is a slab of 6 layers. The first 3 layers are mobile whiles the last three layers are fixed. I would like to add adsorbates at the FCC ...
Nana Kofi Boakye's user avatar
3 votes
1 answer
208 views

How do you write an .xyz file with the information of cell as comment in the Atomic Simulation Environment?

I want to convert the OUTCAR file to a file of xyz (not extxyz) format. The informaiton of lattice (or cell) is stored in the comment line (like extxyz format). Can this be done with the help of ase ? ...
peng liu's user avatar
3 votes
1 answer
149 views

Saving forces from ASE Molecular Dynamics calculations

I have run some molecular dynamics calculations with a pretrained machine-learning potential (M3GNet) which uses the ASE MolecularDynamics calculator. My goal is to compare the results (energies and ...
Jingyang Wang's user avatar
2 votes
2 answers
199 views

Basic MD in ASE

I am testing ASE with a basic H2 MD simulation. I am reading the input file from a xyz file (generated with Packmol), I set pbc True . Then, I relax the system with BFGS and move to NVT and NPT ...
Marco Di Gennaro's user avatar
6 votes
1 answer
194 views

Clustering Algorithms with Periodic Boundary Conditions

I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species. Specifically, I am looking for clustering ...
Saha_1994's user avatar
  • 969
5 votes
1 answer
467 views

Visualise bonds in ASE

I want to visualize an MD trajectory produced with ASE. ase.visualize.view produces an output for atoms and trajectories. I am not able to show the bonds between atoms. For atoms, I can use this in ...
Marco Di Gennaro's user avatar
4 votes
2 answers
268 views

Copper FCC structure using ASE (Atomic Simulation Environment) library in python

I want to create a FCC structure using ASE (atomic simulation environment). I have define the all the required parameter correctly but at the time when i add GPAW calculator. The output of the program ...
Akshit Dhillon's user avatar
2 votes
1 answer
404 views

Create a SMILES from ASE Atoms

I am trying to create a SMILES representation starting from a .xyz molecule description (positions + symbols) read as ASE Atoms. How can I convert a given molecule as a SMILES string ?
Julien Blanchon's user avatar
5 votes
0 answers
85 views

Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)

I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
Saha_1994's user avatar
  • 969
5 votes
1 answer
691 views

Atomic Simulation Environment (ASE) Modelling. Adding additional layer

Beginners here, to ASE. I've create a 2x2x2 supercell of TiO2 from unit cell (.cif file obtained from LegacyMaterialsProject ) using ASE. The script code is attached as follows. The outcome is shown ...
ASA's user avatar
  • 53
1 vote
1 answer
165 views

Use Atomic Simulation Environment to set DFT+U parameters with Quantum Espresso

I wish to set the DFT+U parameters (ideally with the Liechtenstein’s formulation) using ASE and the Quantum Espresso calculator. I have seen that the format for QE has been updated to give the Hubbard ...
Wychh's user avatar
  • 2,147
4 votes
2 answers
298 views

Ionic relaxation with ASE (Atomic Simulation Environment)

I want to do an ionic relaxation of just the ions inside my unit cell (not the cell dimensions), with Quantum Espresso through ASE. However, I have only been able to find structure optimization ...
Wychh's user avatar
  • 2,147
4 votes
1 answer
537 views

How to build a unit cell in ASE?

As a basic example, I want to build a defect MgO unit cell within ASE. From VASP the input is simple: ...
Wychh's user avatar
  • 2,147